Soft-templating synthesis provides an effective route to prepare ordered mesoporous carbons (MCs) that can be used for supercapacitors. During this process, the cross-linking of carbon precursors is critical to obtain tailored pore structural MCs, thus careful selection of appropriate cross-linking agents is required. Despite the shift from the prevailing cross-linker formaldehyde to its more environmentally friendly alternatives, detailed understanding on the influence of different cross-linking agents on templating synthesis is still lacking. Therefore, it remains challenging to draw a conclusion regarding which cross-linker can effectively enable an ideal cross-linking and a robust templating synthesis of ordered MCs. This work presents a systematic study, by comparing three typical cross-linkers (formaldehyde, glyoxal, and glyoxylic acid), on the pore architecture, surface functionality, and electrochemical performance of resulting MCs. Both the type of cross-linker and its ratio with precursor monomer were found to be crucial for the pore architecture and electrochemical performance of resulting MCs. Glyoxal showed to be a promising cross-linker for easily generating ordered mesopores between 3.3-6.1 nm when the molar ratio between cross-linker and carbon precursor ranged from 1 to 2, whereas glyoxylic acid and formaldehyde induced interrupted or disordered mesopores. When the resulting MCs were used as supercapacitor electrodes, those cross-linked with glyoxal also led to overall higher capacitance in both 6 M KOH aqueous and ionic liquid [N2220][NTf2]/acetonitrile electrolytes thanks to the dominance of ordered mesopore channels, especially MC prepared at glyoxal/precursor molar ratio of 1.5. These findings on the effect of cross-linking on templating synthesis can be used to guide the customisation of MCs for supercapacitors and other applications by smartly choosing a suitable cross-linking agent and its ratio with the precursor.